[Biojava-l] Programming hang while trying to do Profile HMM

[allanlee]

Hi, Good day!
 
I am trying to follow the exmaple given in http://www.biojava.org/docs/bj_in_anger/profileHMM.htm
 
but when I tried to run it, it just hang there. It hang there when I call:
 
DP dp = DPFactory.DEFAULT.createDP(hmm);
 
-------------------------------------------------------------------------------------------------------------------------------
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.dist.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.Sequence;
public class PHMM 
{
  public PHMM()
  {
    try
    {
      /*
       * Make a profile HMM over the DNA Alphabet with 12 'columns' and default
       * DistributionFactories to construct the transition and emmission
       * Distributions
       */
      ProfileHMM hmm = new ProfileHMM(DNATools.getDNA(),
                                      12,
                                      DistributionFactory.DEFAULT,
                                      DistributionFactory.DEFAULT,
                                      "my profilehmm");
      //create the Dynamic Programming matrix for the model.
      DP dp = DPFactory.DEFAULT.createDP(hmm);
      //Database to hold the training set
      //SequenceDB db = new HashSequenceDB();
      //Load the training set
      //System.out.println("name=["+db.getName()+"]");
    }catch (Exception e)
    {
      e.printStackTrace();
    }
  }
  public static void main(String[] args)
  {
    PHMM phmm = new PHMM();
    System.out.println("exit");
  }
}
-------------------------------------------------------------------------------------------------------------------------------
FYI, I am using the follow libraries:
 
a)biojava-1.30-jdk14.jar 
b)bytecode-0.92.jar
c)xerces
 
Btw, as I am new to profileHMM, do you have more complete sample that I can work around??
 
I appreciate your help very very much!! Thanks!
 
 
best regards,
@llan
 


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